tomodrgn.mrc

Classes and functions for loading and writing .mrc(s) headers and data.

Generally adheres to the MRC2014 Update 20141 specification.

• MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography

• https://www.ccpem.ac.uk/mrc_format/mrc2014.php

• ccpem/mrcfile

Deviations from this standard include:

1. any data in the extended header is read (and maintained for later writing), but is not interpreted or used in any way;

2. the machst attribute of the header is unpacked as a byte string (e.g b`DA`) rather than as an array of uint8 (e.g. [68, 65, 0, 0]);

3. the label attribute of the header is unpacked as a concatenated byte string rather than as an array of byte strings for all 10 80-character labels that may exist

Prefer the following uses:

• interfacing with MRC headers: mrc.MRCHeader.parse() or mrc.parse_header()

• loading an entire MRC file into memory: mrc.parse_mrc()

• loading a list of MRC files into memory: mrc.parse_mrc_list()

• lazily loading a single image from an MRC file: mrc.LazyImage

• lazily loading a group of images from an MRC file: mrc.LazyImageStack

• writing an MRC file to disk: mrc.write()

Functions

parse_header	Convenience function to create an MRCHeader object given an MRC file name
parse_mrc	Load an entire MRC file into memory as either a numpy array or a list of LazyImages
parse_mrc_list	Load the MRC file(s) specified in a text file into memory as either a numpy array or a list of LazyImages.
write	Write a data array to disk in MRC format.

Classes

LazyImage	Class to lazily load data from an MRC file on-the-fly
LazyImageStack	Efficiently load a particle stack from an NxDxD stack.mrcs file on-the-fly.
MRCHeader	Class to parse the header of an MRC file and to write a new MRC header to disk.